Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to
use an externally generated pqr file. The current mechanism for calling
pdb2pqr from within the APBS Tool results in pdb2pqr running under the same
python as pymol.
Jack
On Mon, Dec 2, 2019 at 5:58 PM Jack Howarth
You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff
and
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff
applied over Pmw_2_0_0.
Jack
Dear all,
I get the following errors when trying to launch the APBS plugin from the
plugins menu
Traceback (most recent call last):
File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 322, in
command = lambda s=self: APBSTools2(s))
File "/home/quyen/Pymol/i
Dear Thomas,
thank you for these short and perfect answers.
1. All fine now.
2. Updated the plugin and the GUI bug is gone. One more thing though.
Whenever I click the button to either set temporary file locations or to set
program locations in APBS GUI window I immediately get a Segmenta
Hi Matic,
1. If you have conflicting (non-unique) file names, you have two options:
a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
b) Set the "auto_rename_duplicate_objects" setting
2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days
a
Dear all,
I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I
use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0.
1. First I tried to perform a couple of APBS calculations through the APBS
plugin window and all went great. Then I did a
Hi Troels,
Many thanks for your email!
I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?
>svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>sv
Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packe
Dear all,
I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source (
http://www.pymolwiki.org/index.php/Linux_Install).
When running the plugin, I can set the grid, but after clicking on Run
APBS, I get the following error:
Unexpected error
Hi,
Those of you interested in APBS-based electrostatics in PyMOL via
Michael Lerner's plugins may be interested in an RPM available at
"http://mccammon.ucsd.edu/~cmura/PYMOL_examples/pymol-0.96apbs-2rh90.i386.rpm";.
It is basically a CVS snapshot of a recent version of PyMOL (v0.96beta5;
05/
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